BSDB

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN I J |I-J| Displacement error 1 15 39 24 339.19 0.14 2 16 36 20 338.42 0.23 3 16 37 21 338.62 0.13 4 17 34 17 338.26 0.15 5 17 35 18 339.88 0.49 6 17 36 19 339.85 0.48 7 18 35 17 340.19 0.35 8 18 36 18 340.19 0.35 9 18 37 19 340.26 0.31 10 18 43 25 340.33 0.27 11 19 34 15 340.25 0.33 12 19 35 16 340.25 0.33 13 20 32 12 340.50 0.48 14 20 33 13 340.27 0.34 15 20 34 14 340.25 0.33 16 20 50 30 338.54 0.47 17 21 32 11 340.53 0.46 18 21 33 12 340.44 0.42 19 22 25 3 746.77 5.90 20 22 31 9 340.86 0.35 21 22 32 10 340.72 0.40 22 23 31 8 340.87 0.34 23 23 32 9 340.81 0.35 24 23 33 10 340.83 0.34 25 23 47 24 340.54 0.19 26 24 30 6 417.73 38.73 27 24 31 7 340.88 0.34 28 25 29 4 633.46 11.43 29 25 30 5 340.91 0.33 30 25 52 27 340.20 0.22 31 26 29 3 676.84 0.49 32 27 52 25 340.42 0.21 33 28 51 23 340.49 0.18 34 28 52 24 340.38 0.19 35 28 53 25 340.33 0.17 36 29 49 20 340.68 0.10 37 29 50 21 340.50 0.17 38 29 51 22 340.33 0.17 39 29 52 23 340.33 0.17 40 30 49 19 340.66 0.09 41 30 50 20 340.44 0.18 42 30 52 22 340.32 0.17 43 31 47 16 340.81 0.05 44 31 48 17 340.76 0.04 45 31 49 18 340.61 0.06 46 32 47 15 340.79 0.03 47 32 48 16 340.75 0.03 48 32 50 18 340.62 0.03 49 33 45 12 435.06 47.02 50 33 46 13 340.85 0.01 51 34 45 11 435.07 47.03 52 34 46 12 435.02 47.04 53 34 48 14 340.73 0.02 54 35 43 8 514.38 8.34 55 35 44 9 436.30 47.32 56 35 45 10 436.19 47.32 57 36 43 7 524.53 13.41 58 36 44 8 436.43 47.31 59 36 45 9 436.35 47.34 60 36 46 10 436.35 47.34 61 37 41 4 642.68 6.88 62 37 42 5 561.54 5.08 63 37 43 6 524.53 13.41 64 38 41 3 674.24 3.56 65 38 42 4 573.73 0.99 66 38 44 6 540.56 5.40 67 46 135 89 357.44 2.44 68 48 136 88 357.67 2.50 69 49 136 87 357.70 2.52 70 49 137 88 357.69 2.52 71 49 138 89 357.69 2.52 72 50 138 88 357.70 2.52 73 51 54 3 687.36 0.99 74 51 60 9 357.72 2.50 75 51 98 47 357.70 2.52 76 51 139 88 357.72 2.51 77 53 98 45 362.00 4.64 78 54 58 4 661.96 4.83 79 54 59 5 599.43 3.58 80 54 60 6 449.00 38.77 81 54 138 84 425.56 1.19 82 54 140 86 392.53 0.29 83 55 58 3 675.53 1.95 84 55 99 44 387.85 2.77 85 55 100 45 447.07 25.29 86 55 101 46 456.81 27.68 87 58 99 41 502.25 10.10 88 59 99 40 502.30 10.12 89 59 129 70 450.91 1.33 90 59 140 81 484.61 1.46 91 59 141 82 458.75 0.77 92 59 142 83 436.38 0.93 93 60 98 38 502.37 10.13 94 60 99 39 502.34 10.12 95 60 139 79 484.88 1.41 96 60 140 80 484.81 1.41 97 61 97 36 502.40 10.13 98 61 98 37 502.37 10.13 99 61 99 38 502.34 10.12 100 61 140 79 484.88 1.41 101 61 141 80 484.85 1.41 102 61 142 81 484.84 1.41 103 62 96 34 502.60 10.16 104 62 97 35 502.45 10.11 105 62 99 37 502.40 10.13 106 62 105 43 502.16 10.05 107 62 108 46 502.17 10.05 108 62 109 47 502.07 10.02 109 62 141 79 484.86 1.41 110 62 142 80 484.85 1.41 111 62 144 82 484.81 1.41 112 63 94 31 502.83 10.21 113 63 95 32 502.71 10.19 114 63 96 33 502.61 10.16 115 63 141 78 484.93 1.41 116 63 142 79 484.88 1.41 117 63 143 80 484.85 1.41 118 63 144 81 484.85 1.41 119 63 196 133 126.83 1.11 120 64 94 30 502.84 10.21 121 64 95 31 502.79 10.22 122 64 109 45 502.26 10.06 123 64 113 49 502.22 9.98 124 64 144 80 484.85 1.41 125 64 146 82 484.75 1.42 126 65 77 12 504.26 10.68 127 65 94 29 502.85 10.21 128 65 143 78 484.94 1.41 129 65 144 79 484.88 1.41 130 65 145 80 484.85 1.41 131 65 146 81 484.84 1.41 132 65 200 135 124.38 0.57 133 66 76 10 504.64 10.57 134 66 77 11 504.28 10.69 135 66 78 12 504.23 10.67 136 66 94 28 503.38 10.26 137 66 95 29 502.98 10.20 138 66 113 47 502.44 10.00 139 66 146 80 484.85 1.41 140 66 148 82 484.75 1.42 141 67 75 8 504.69 10.59 142 67 76 9 504.64 10.57 143 67 77 10 504.54 10.57 144 67 145 78 484.93 1.41 145 67 146 79 484.88 1.41 146 67 147 80 484.84 1.41 147 67 148 81 484.82 1.41 148 68 75 7 504.69 10.59 149 68 76 8 504.68 10.59 150 68 78 10 504.58 10.57 151 68 119 51 501.70 9.62 152 68 148 80 484.85 1.41 153 68 150 82 484.63 1.38 154 68 172 104 238.86 0.96 155 69 75 6 504.70 10.59 156 69 147 78 484.91 1.42 157 69 148 79 484.87 1.41 158 69 149 80 484.85 1.41 159 69 150 81 484.82 1.41 160 70 73 3 674.86 1.58 161 70 150 80 484.84 1.41 162 70 151 81 484.80 1.40 163 71 151 80 484.86 1.41 164 74 174 100 238.78 0.93 165 74 176 102 238.72 0.93 166 75 174 99 238.74 0.92 167 75 175 100 238.25 1.02 168 76 172 96 238.78 0.93 169 76 173 97 238.74 0.93 170 76 174 98 238.06 1.11 171 76 175 99 235.94 0.46 172 77 94 17 507.67 8.27 173 77 172 95 238.87 0.98 174 77 173 96 238.61 0.88 175 77 175 98 226.38 1.79 176 77 178 101 174.41 9.33 177 77 200 123 127.72 0.90 178 78 95 17 507.66 8.28 179 78 117 39 504.92 8.58 180 78 119 41 503.79 8.45 181 78 148 70 484.79 1.43 182 78 170 92 239.03 0.99 183 78 171 93 238.94 0.97 184 78 172 94 238.72 0.93 185 79 92 13 512.47 6.00 186 79 93 14 507.82 8.31 187 79 94 15 507.68 8.27 188 79 95 16 507.67 8.27 189 79 170 91 238.99 0.98 190 79 171 92 238.89 0.96 191 79 173 94 238.59 0.86 192 79 178 99 178.01 7.55 193 79 182 103 146.02 3.68 194 79 197 118 127.72 0.90 195 80 91 11 519.96 4.20 196 80 92 12 518.37 3.89 197 80 93 13 509.07 7.69 198 80 95 15 507.68 8.28 199 80 116 36 505.70 8.19 200 80 117 37 505.56 8.13 201 80 168 88 239.35 1.03 202 80 169 89 239.06 1.01 203 80 170 90 239.00 0.98 204 81 90 9 520.91 3.79 205 81 91 10 519.47 4.03 206 81 92 11 519.14 4.12 207 81 168 87 239.38 1.04 208 81 169 88 239.06 1.01 209 81 171 90 239.01 0.98 210 81 189 108 130.41 0.29 211 81 191 110 129.80 0.35 212 82 90 8 520.96 3.80 213 82 91 9 520.20 4.08 214 82 167 85 239.47 1.04 215 82 168 86 239.41 1.03 216 83 88 5 614.84 6.76 217 83 89 6 531.29 1.28 218 83 90 7 523.74 2.46 219 84 87 3 670.19 0.35 220 84 88 4 636.48 13.26 221 84 89 5 565.44 5.58 222 84 91 7 530.62 1.44 223 84 93 9 530.62 1.44 224 85 88 3 673.62 5.31 225 87 91 4 682.66 1.67 226 87 192 105 129.88 0.42 227 90 191 101 129.80 0.35 228 90 192 102 129.79 0.35 229 91 192 101 129.66 0.36 230 92 171 79 238.99 0.98 231 92 182 90 137.29 0.48 232 92 185 93 130.38 0.28 233 92 191 99 129.78 0.35 234 92 192 100 129.62 0.36 235 92 193 101 129.24 0.39 236 92 194 102 129.24 0.38 237 93 194 101 128.98 0.28 238 93 197 104 127.39 0.88 239 94 196 102 127.42 0.88 240 94 197 103 126.91 1.07 241 94 200 106 126.81 1.12 242 95 113 18 505.83 8.23 243 95 116 21 505.41 8.01 244 95 117 22 505.06 7.78 245 96 112 16 505.88 8.24 246 96 116 20 505.30 7.70 247 97 112 15 505.91 8.09 248 98 111 13 528.62 0.69 249 99 103 4 646.66 5.50 250 99 105 6 554.37 3.85 251 99 108 9 524.75 1.24 252 99 142 43 484.92 1.39 253 100 103 3 678.40 0.47 254 100 111 11 529.64 1.06 255 103 107 4 659.35 2.73 256 103 108 5 658.38 2.25 257 103 111 8 645.79 1.90 258 104 107 3 668.61 5.26 259 104 108 4 667.16 0.99 260 105 108 3 677.82 0.18 261 105 109 4 666.98 1.09 262 105 142 37 484.94 1.41 263 106 109 3 680.72 3.02 264 106 110 4 669.73 2.48 265 106 123 17 488.61 0.48 266 106 126 20 487.84 0.05 267 107 110 3 686.21 0.27 268 107 111 4 669.74 2.48 269 108 111 3 680.69 3.00 270 108 112 4 669.33 2.68 271 109 112 3 684.95 2.44 272 109 113 4 669.08 0.84 273 109 123 14 489.15 0.59 274 109 144 35 484.89 1.41 275 109 146 37 484.80 1.40 276 110 113 3 684.09 4.88 277 110 114 4 668.32 0.47 278 110 121 11 500.57 6.25 279 110 122 12 489.17 0.59 280 110 123 13 489.16 0.59 281 110 146 36 484.84 1.40 282 111 114 3 680.49 4.86 283 111 115 4 663.74 0.55 284 112 115 3 671.79 1.28 285 112 116 4 662.82 0.09 286 112 166 54 239.41 1.03 287 113 116 3 685.29 2.43 288 113 117 4 662.74 0.04 289 113 118 5 657.14 2.06 290 113 119 6 640.93 3.70 291 113 121 8 574.65 15.74 292 113 146 33 484.84 1.41 293 113 148 35 484.71 1.40 294 114 117 3 673.21 0.57 295 114 118 4 640.91 2.90 296 114 119 5 626.30 3.57 297 114 120 6 595.24 5.48 298 114 160 46 239.68 1.02 299 115 160 45 239.67 1.02 300 115 161 46 239.50 1.04 301 115 162 47 239.50 1.04 302 116 160 44 239.68 1.02 303 116 166 50 239.42 1.03 304 116 168 52 239.02 0.98 305 116 170 54 238.97 0.97 306 117 158 41 239.96 0.98 307 117 160 43 239.68 1.02 308 117 170 53 238.97 0.97 309 118 158 40 239.94 0.98 310 118 159 41 239.85 0.96 311 118 160 42 239.68 1.02 312 119 148 29 484.73 1.40 313 119 155 36 240.34 0.95 314 119 158 39 239.95 0.98 315 120 154 34 240.43 0.91 316 120 155 35 240.36 0.94 317 121 146 25 484.89 1.41 318 121 147 26 484.86 1.41 319 121 148 27 484.75 1.36 320 122 146 24 484.93 1.41 321 122 147 25 484.88 1.42 322 123 144 21 485.00 1.40 323 123 145 22 484.95 1.40 324 123 146 23 484.88 1.41 325 124 145 21 484.96 1.41 326 124 147 23 484.90 1.40 327 125 144 19 485.06 1.39 328 125 145 20 484.97 1.41 329 126 142 16 485.15 1.37 330 126 143 17 485.08 1.39 331 126 144 18 485.06 1.39 332 127 142 15 485.17 1.36 333 127 143 16 485.10 1.38 334 128 142 14 485.21 1.35 335 129 140 11 485.35 1.33 336 129 141 12 485.30 1.33 337 129 142 13 485.24 1.35 338 130 140 10 485.35 1.33 339 130 141 11 485.34 1.34 340 130 143 13 485.29 1.33 341 131 134 3 687.71 0.56 342 131 139 8 485.48 1.37 343 131 140 9 485.37 1.33 344 132 139 7 485.49 1.37 345 132 141 9 485.48 1.36 346 132 196 64 123.50 0.54 347 133 136 3 684.92 2.99 348 133 137 4 619.51 9.85 349 134 137 3 683.69 2.38 350 141 196 55 124.34 0.55 351 148 155 7 392.00 74.88 352 149 152 3 688.29 0.09 353 149 155 6 392.01 74.89 354 150 155 5 392.01 74.89 355 152 155 3 676.11 1.53 356 152 156 4 674.19 0.57 357 153 156 3 674.19 0.57 358 155 158 3 677.99 0.98 359 162 166 4 565.31 0.04 360 163 166 3 652.68 4.43 361 173 178 5 575.74 5.82 362 173 181 8 371.23 89.09 363 173 182 9 371.23 89.09 364 173 185 12 351.39 98.98 365 174 177 3 697.36 2.93 366 174 178 4 628.87 9.04 367 174 181 7 572.44 0.86 368 175 178 3 665.70 1.96 369 175 204 29 127.59 0.89 370 177 180 3 686.18 4.87 371 177 181 4 658.34 3.77 372 178 181 3 665.66 0.10 373 178 182 4 654.74 5.57 374 178 200 22 129.31 0.25 375 178 201 23 129.08 0.36 376 178 204 26 127.66 0.92 377 179 182 3 679.79 0.18 378 179 183 4 665.51 0.03 379 179 198 19 129.39 0.30 380 179 201 22 129.13 0.34 381 179 202 23 129.13 0.34 382 179 205 26 127.61 0.90 383 180 183 3 678.72 0.32 384 180 184 4 664.83 0.32 385 181 184 3 667.51 0.04 386 181 185 4 659.22 2.49 387 182 185 3 667.89 1.22 388 182 186 4 664.80 0.31 389 182 193 11 129.76 0.33 390 182 197 15 129.74 0.34 391 182 201 19 129.22 0.39 392 183 186 3 672.44 1.06 393 183 187 4 664.78 0.32 394 184 187 3 674.25 1.90 395 184 188 4 667.86 1.23 396 185 188 3 671.25 3.40 397 185 189 4 664.76 0.32 398 185 191 6 646.56 2.16 399 186 189 3 670.42 1.76 400 186 190 4 646.56 2.16 401 186 191 5 641.36 0.44 402 186 193 7 574.37 7.28 403 187 190 3 687.47 5.79 404 193 197 4 668.21 8.79 405 193 198 5 653.57 1.48 406 194 197 3 676.36 4.72 407 194 198 4 677.00 4.41 408 195 198 3 677.60 4.11 409 195 199 4 677.00 4.41 410 196 199 3 677.01 4.41 411 196 200 4 669.29 0.55 412 197 200 3 677.54 4.15 413 197 201 4 660.68 0.34 414 198 201 3 671.50 1.12 415 198 202 4 650.52 2.98 416 199 202 3 674.78 8.49 417 199 203 4 662.16 2.90 418 200 203 3 682.12 4.96 419 200 204 4 670.09 1.05 420 201 204 3 682.12 4.96 421 201 205 4 670.10 1.05 422 202 205 3 683.12 4.77 423 202 206 4 670.90 1.34 424 203 206 3 670.91 1.34 425 203 207 4 670.90 1.34 426 204 207 3 673.95 0.17 427 204 208 4 656.48 2.63 428 205 208 3 673.94 0.18 429 205 209 4 645.36 4.21 430 208 211 3 693.41 0.63 431 210 213 3 662.86 2.83 432 210 214 4 664.60 1.97 433 211 215 4 682.80 0.70 434 212 215 3 686.57 2.58 435 212 216 4 670.90 1.17 436 213 216 3 685.11 3.75 437 213 217 4 685.20 3.77 438 214 217 3 707.09 5.80 439 215 218 3 693.29 0.28 440 215 219 4 687.63 2.56 441 216 219 3 701.30 3.76